#bioc2022

2022-03-08

Charlotte Soneson (14:18:35): > @Charlotte Soneson has joined the channel

Charlotte Soneson (14:18:36): > set the channel description: Discussions related to BioC2022, which will take place in hybrid form in Seattle/online on July 27-29, 2022

Nils Eling (14:27:25): > @Nils Eling has joined the channel

Marcel Ramos Pérez (15:10:30): > @Marcel Ramos Pérez has joined the channel

Stephanie Hicks (15:35:53): > @Stephanie Hicks has joined the channel

Stephanie Hicks (15:36:06): > :wave:

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Noriaki Sato (19:51:57): > @Noriaki Sato has joined the channel

2022-03-09

Federico Marini (17:19:04): > @Federico Marini has joined the channel

2022-03-11

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Ana Beatriz Villaseñor Altamirano (10:12:50): > @Ana Beatriz Villaseñor Altamirano has joined the channel

Ana Beatriz Villaseñor Altamirano (10:22:00): > Hi everyone! A few years ago I attended in person #bioc20219 and I had an amazing experience. I’m not developing any package right now, but I wondered if you have any track for #UseBioC, in which we can talk about how we are using BioC packages? It’d be nice to have a space for meeting developers, and as developers to talk to users, maybe even create collaborations based on users’ needs??

2022-03-16

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2022-03-18

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2022-03-24

Andres Wokaty (12:28:36): > Is there a specific format for the short demos? Someone who submitted an abstract asked how they should prepare “a github source site and an associated docker”? I wasn’t sure if I should point them to past examples or if there was specific documentation somewhere that I didn’t know about.

2022-03-25

Charlotte Soneson (02:49:51) (in thread): > The GitHub+Docker is mostly for the long workshops where we expect a certain level of interactivity and for people to be able to follow along (and they would be prepared usinghttps://github.com/seandavi/BuildABiocWorkshop). Demos are not required to be interactive, but if they are, I would use the same template as for the workshops.

2022-03-29

Andres Wokaty (17:39:05): > Is it possible to leave the submission site open a little longer? I think Herve and Nitesh want to submit abstracts but didn’t know that it took time for their openreview credentials to get approved. Or should I submit for them since I already have an approved account?:slightly_smiling_face:

2022-03-30

Charlotte Soneson (01:44:59) (in thread): > Looks like this worked out - usually the approval is pretty quick:slightly_smiling_face:

Federico Marini (08:32:06): > General thoughts about the present and future of hybrid conferences ->https://www.biorxiv.org/content/10.1101/2022.03.18.484941v1 - Attachment (bioRxiv): Hybrid conferences: opportunities, challenges and ways forward > Hybrid conferences are in-person events that are also accessible online. This type of meeting format was rare pre-COVID-19 but started to become more common recently given the asynchronous global progression of the pandemic and the uneven access and distribution of vaccines that led to a large proportion of participants being unable to attend international conferences in person. Here we report the organization of a middle-sized (581 participants: 159 onsite, 422 online) international hybrid conference that took place in France in September 2021. We highlight particular organizational challenges inherent to this relatively new type of meeting format. Furthermore, we surveyed both in-person and online participants to better understand their conference experience and to propose improvements based on the feedback received. Finally, we compare the advantages and disadvantages of three types of conferences (onsite-only, online-only and hybrid) and suggest that hybrid events should be favored in the future because they offer the most flexibility to participants. We conclude by proposing suggestions and ways forward to maximize accessibility and inclusivity of hybrid conferences. ### Competing Interest Statement The authors have declared no competing interest.

2022-04-07

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2022-04-14

Nicole Ortogero (19:19:45): > @Nicole Ortogero has joined the channel

2022-04-19

Tim Triche (11:39:18): > @Tim Triche has joined the channel

2022-04-22

Jonas Schulte-Schrepping (08:42:16): > @Jonas Schulte-Schrepping has joined the channel

2022-04-24

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2022-05-04

Leonardo Collado Torres (16:56:34): > Hi! Do you know if BioC2022 will be at the FHCRC? Like in other years. Akahttps://www.google.com/maps/place/Fred+Hutchinson+Cancer+Research+Center/@47.6272634[…]24d2553ecd:0xbd94de9cd960bdd0!8m2!3d47.6272634!4d-122.3314858? > > We need to submit a pre-approval form at our workplace which includes trying to price out a hotel. - Attachment (google.com): Fred Hutchinson Cancer Research Center · 1100 Fairview Ave N, Seattle, WA 98109 > ★★★★★ · Research institute

Leonardo Collado Torres (16:57:01): > Also, other times there was a hotel discount, which well, I’m not sure there will be one this year.

2022-05-06

Tim Triche (17:52:57): > Seattle Children’s, not too far from FHCRC but closer to downtown

2022-05-07

Leonardo Collado Torres (09:45:19): > Ok, thanks Tim!

2022-05-08

Leonardo Collado Torres (10:15:40): > hm… I see many options:stuck_out_tongue:Do you have an exact location@Tim Triche(or anyone else)? - File (PNG): Screen Shot 2022-05-08 at 10.15.06 AM.png

Leonardo Collado Torres (10:16:04): - File (PNG): Screen Shot 2022-05-08 at 10.15.58 AM.png

Leonardo Collado Torres (10:17:39): > nvm, I found it athttps://bioc2022.eventbrite.com/ - Attachment (Eventbrite): BioC2022 Annual Conference > Registration is now open. Please read below for the types of tickets available and how to register.

Leonardo Collado Torres (10:17:57): > https://bioc2022.bioconductor.org/doesn’t have that info (which is where I was looking at)

Leonardo Collado Torres (10:18:30): > https://goo.gl/maps/Emrs2ZjscmUCkDm49 - Attachment (google.com): Seattle Children’s Research Institute: Building Cure · 1920 Terry Ave, Seattle, WA 98101 > ★★★★★ · Research institute

Tim Triche (10:25:37): > I used to just stay at the hostel if I wasn’t presenting. I probably would again if not for my lab (need to pretend to be respectable)

Tim Triche (10:27:54): > @Marc RJ Carlsonis the man with all the answers tbh. This Seattle business was mostly his idea:wink:

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Tim Triche (10:29:13): > Many of the sessions will be at 818 Stewart and (other nearby building whose name I forget). More importantly, there’s a good cheap Vietnamese place near both

2022-05-09

Marc RJ Carlson (11:53:30): > OK, so I should probably have anticipated this question. There are TWO “major” campuses for Seattle Children’s (and there are other smaller ones too, but: lets not make things even more complicated). There is a hospital campus over by Sand Point (which is NOT where we are planning to host Bioconductor this summer), and then there is a research campus downtown (which IS where we plan to host the conference this summer) The address for the Cure building that someone posted above is at the downtown research campus. > > There are multiple reasons why we would want to use the research campus. But at least one that I am sure you can all appreciate is that it’s in the middle of Seattle where all the ‘interesting’ parts of town are. And unlike the hospital, it’s actually very easy to get to the research campus via the light rail system, and there are plenty of good places to eat etc.

Leonardo Collado Torres (23:47:43): > Thanks for the info Marc!

2022-05-17

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2022-05-19

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2022-05-26

Aidan Lakshman (11:15:25): > :raised_hands:I saw that theBioc2022 scheduleis posted! Thanks for all the work the organizers are doing to make this event possible; looking forward to seeing lots of great presentations :D - Attachment (bioc2022.bioconductor.org): Schedule > Schedule

Aidan Lakshman (12:17:32): > Any suggestions for hotels/places to stay for the conference?

Cindy Fang (14:53:12): > @Cindy Fang has joined the channel

2022-06-01

Nicole Ortogero (23:36:34): > I believe I saw a list of hotels linked on the registration page.

2022-06-09

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2022-06-13

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2022-06-21

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2022-07-07

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Martin Morgan (15:38:05): > I’ll present apackage demoat Bioc2022. The email from Erica (:wave:) mentioned “…not using the Orchestra platform…” but I would like to use the Orchestra platform. Are there instructions for that? Also, I’ll present a similar demo at another venue; can I re-use my Orchestra presentation outside Bioc2022?

Charlotte Soneson (16:32:49) (in thread): > If you want to use Orchestra, please follow the instructions athttps://github.com/seandavi/BuildABiocWorkshopto format your demo as an R package. Once you have a draft done (the earlier the better to iron out any technical issues, you can still update the content at any time), let us know by opening a ‘New Orchestra Workshop’ issue athttps://bit.ly/new_orchestra, and it will be added to Orchestra. Regarding using the presentation outside BioC2022, I don’t see a problem with that - as far as I know the workshops will stay up on Orchestra (cc@Sean Davisand@Jenny Drnevichfor any additional comments here).

Jenny Drnevich (16:46:36) (in thread): > @Martin Morganit seems like you are not quoting last week’s email from Erica with the subject “Package Demo Speaker Information - Please read”? We did not intend package demos to be on Orchestra (although they were never prohibited) but now that we’ve learned that you cannot use your own laptop to present, many more workshop demos might use Orchestra. Just remember that the shorter demo time was because people were not going to be logging on and following along.

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Sean Davis (16:52:31): > For anyone (@Martin Morgan) who wants to use Orchestra to present a package demo, I just need a docker container that has that package installed and presents an RStudio (or another web ui like Jupyter, etc.). If you want to follow the BuildABiocWorkshop approach, feel free. If you’d rather use your own tools to build the container, that works, also. Then, just submit a github issue here:https://bit.ly/new_orchestra - Attachment (GitHub): Build software better, together > GitHub is where people build software. More than 83 million people use GitHub to discover, fork, and contribute to over 200 million projects.

Martin Morgan (16:53:31) (in thread): > Hi@Jenny Drnevich– Yes the email had that title. Even though people are not following along, it stills seems value to provide a resource for reference. This is the email from 5 July > > Thank you for participating in the BioC2022 Annual Conference. Below is the information you need to participate in this virtual meeting. If you have not registered for the conference, please do so by July 8th. > > * Please check the schedule onhttps://bioc2022.bioconductor.org/schedule/to see your speaking time.. Please note that******times could shift******. We will do our best to notify you of any changes if this occurs. > * Please join your session about 10 minutes prior to the start so we can test your video and audio. > * You will meet the chair and hosts of the session and discuss how the session will proceed. > * Your session is 45 minutes. > * You should plan about 35 minutes of speaking time, to allow for questions from the audience. > * The hosts can assist with questions. > * We plan to have a rehearsal prior to the conference to familiarize you with the platform. > * We will send you an invite to that when the date is settled. > * You will receive an invitation to a Webex Meeting for your session. Please be on the lookout for this email. > * If you want attendees to follow along and you are not using the Orchestra platform,please send us any URLs in advance at**** ****conference@bioconductor.orgso we can ensure that it is not blocked by the firewall. > * If you wish to pre-record your talk, please follow the instructions in the attached PreRecord Instructions pdf. Please upload your video tohttps://drive.google.com/drive/folders/1sTIyjRzVOZH01ySFcKIHWq5dXhU2vcyR?usp=sharingno later than Monday July 25th. > > > If you have any questions, feel free to contact us atworkshop@bioconductor.org. > > We look forward to seeing you at the conference! - Attachment (bioc2022.bioconductor.org): Schedule > Schedule

Jenny Drnevich (16:56:25) (in thread): > It was the “not using the Orchestra platform” part that confused me because the email seemed to me to be the opposite. I’m just now starting on my demo presentation and will have to think about what will be easiest…

2022-07-08

Sean Davis (07:58:22) (in thread): > By the way, adding something to Orchestra need not be associated with the conference. I’m happy to add at any time for a course you want to teach, etc.

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2022-07-14

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2022-07-15

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2022-07-18

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2022-07-20

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2022-07-22

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Erica Feick (18:02:08): > The countdown to BioC2022 has begun! Emails were sent out to all attendees today with instructions to login to the virtual platform. You can download the mobile app on theApp StoreorGoogle Play, or login on your computer. - Attachment (App Store): ‎Socio Event App > ‎Socio (now part of Webex) takes your event experience to the next level. The Socio app serves as your digital networking portal, event guide, and content hub. Socio will be rebranded as Webex Events and this will be reflected in the app later this year. Socio serves as a digital event guide and con… - Attachment (play.google.com): Socio Event App - Apps on Google Play > Events, Meetings, and Conferences

2022-07-24

Jenny Drnevich (18:15:06): > @Sean Davishttp://app.orchestra.cancerdatasci.org/has been giving a “404 page not found” for over a week. Is everything OK?

Sean Davis (20:43:28) (in thread): > Last-minute updates. It is up now.

2022-07-25

Jenny Drnevich (08:34:05) (in thread): > @Sean DavisI am seeing 3 instances of some workshops (Epidemiology and Tidy Transcriptomics) - File (PNG): image.png

Jenny Drnevich (08:36:31) (in thread): > Maybe they are past versions? Although Tidy Transcriptomics has two versions starting with BioC2022.

Sean Davis (09:19:46) (in thread): > I think I got those cleaned up by prefixing with the conference identifier. I need to add another field to capture the conference collections. Thanks for catching.

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2022-07-26

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Martin Morgan (15:41:31) (in thread): > @Sean Davisthis has been a great experience for me – familiar (enough; actually, I had to do quite a bit of learning…) tools leading to very functional product! I want my tutorial (“Accessing Human Cell Atlas..”) listed athttp://app.orchestra.cancerdatasci.org/1to link to thegithub.iopagehttps://mtmorgan.github.io/ExploringHCACxG/, rather than the GitHub repository. My main question is, where should I report issues / find documentation / etc on that? - Attachment (mtmorgan.github.io): ExploringHCACxG > Human Cell Atlas data sets can be discovered, previewed, and downloaded using the HCA data portal (https://data.humancellatlas.org/explore/projects) and cellxgene (https://cellxgene.cziscience.com/) web sites. The hca and cellxgenedp R / Bioconductor packages provide a more flexible and reproducible approach to using this data. In particular the packages allow direct integration of HCA data sets into the OSCA (https://bioconductor.org/books/release/OSCA/) single-cell analysis workflows in R / Bioconductor.

Sean Davis (17:11:17) (in thread): > Hi,@Martin Morgan. Should be changed now. For the time being, I’m using the github orchestra-contributions site for discussion of particular submissions.

Sean Davis (17:12:15) (in thread): > Code for Orchestra is being streamlined and organized around Helm charts. When that process is complete, the idea is to support feature requests through the github repo.

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Jenny Drnevich (17:23:30) (in thread): > @Levi WaldronWhere can@Martin Morgansubmit a pull request to also get the github and io pages added tohttps://bioc2022.bioconductor.org/schedule/? I thought I booked-marked it but I can’t find it nor is it in the notes from today’s meeting - Attachment (bioc2022.bioconductor.org): Schedule > Schedule

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2022-07-27

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Charlotte Soneson (00:52:52) (in thread): > Links to GitHub etc can be added in the corresponding yaml file here:https://github.com/Bioconductor/BioC2022/tree/master/data/abstracts. (‘github’ = source, ‘details’ = renderedgithub.iopage or similar)

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Charlotte Soneson (08:15:36) (in thread): > Re:point_up:(not Orchestra), I just made a PR to add some links to more demos/workshops, including this one, to the BioC2022 website (https://github.com/Bioconductor/BioC2022/pull/47).

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Andres Wokaty (11:00:29): > Hi, we’re working on a conference summary. If you’re interested in contributing by taking notes, you can see instructions and take notes athttps://docs.google.com/document/d/1xqVo9l6z5Tb7_gE0QJXExn9T-12E2XehgwGeRruQ0hA/edit#.

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Jenny Drnevich (11:16:18): > Workshop and Package Demo presenters: If you have links you would like us to put onhttps://bioc2022.bioconductor.org/workshops/, please put them in a thread and we will get them in! - Attachment (bioc2022.bioconductor.org): Workshops & package demos > Workshops & package demos

Vince Carey (11:55:37): > Here are slides for opening talkhttps://docs.google.com/presentation/d/1KVtjAb3o_-4dFhxix1NHlKQ8UnTfU22mRA_7kbaJO7Y/edit?usp=sharing - File (Google Slides): Bioc2022Opener

Tyrone Lee (11:58:40): > I have not received an email yet about how to view the event. I think I’ve only gotten the eventbrite ticket.

Jared Andrews (12:00:10): > @Tyrone Lee - Attachment: Attachment > You can use this link and sign in with the email you registered with. Click this link

Nils Eling (12:22:06) (in thread): > Hey, thanks for that! For the “A Framework For Multiplexed Image Processing And Spatial Analysis” Could you please addhttps://github.com/BodenmillerGroup/demosas Source andhttps://bodenmillergroup.github.io/demos/as Details?

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Leonardo Collado Torres (15:52:18): - File (JPEG): Image from iOS

Ryan C. Thompson (15:59:28): > Is there anything we need to do prior to the workshops to set up, or will any be covered during the workshop?

Lori Shepherd (16:02:10): > You can start an orchestra session awhile. There is a link in the announcement section of the platform

Sean Davis (16:13:11): > Orchestra is athttp://orchestra.cancerdatasci.org. Login and then you can start any workshop that you like. Start with the login and then when you get to the workshop (online or in person), the person leading will tell you how to search for the workshop of interest.

Tim Triche (17:31:01): > orchestra is having some issues onsite fwiw

Sean Davis (17:31:33) (in thread): > In what way?

Tim Triche (17:31:56) (in thread): > 403 error and getting blocked by SCRI for the presenters

Tim Triche (17:32:04) (in thread): > actually audience just got a similar 403 error

Tim Triche (17:32:15) (in thread): > some people are having it work well, others not

Tim Triche (17:32:40) (in thread): > part of the issue is a SCRI firewall issue it seems

Tim Triche (17:33:06) (in thread): > orchestra has obtained a Bad Reputation:tm:somehow for SCRI’s firewall.:shrug:

Leonardo Collado Torres (17:33:14) (in thread): > yeah, that’s what people are saying on thenullrangessession I’m at (I was referring to the firewall part)

Tim Triche (17:33:53) (in thread): > same session for me fwiw (2nd row)

Leonardo Collado Torres (17:34:18) (in thread): > I’ll say hi later ^^

Sean Davis (17:35:08) (in thread): > Thanks. Not sure what I can do. I’m seeing 186 currently-running sessions, including 29 nullranges sessions.

Leonardo Collado Torres (17:41:00) (in thread): > I’m trying to join it now, but I only getBad gatewaymessages. > > It works perfectly if I log in to my JHU (Hopkins) VPN - File (PNG): Screen Shot 2022-07-27 at 2.39.42 PM.png - File (PNG): Screen Shot 2022-07-27 at 2.39.26 PM.png

Lori Shepherd (17:42:31) (in thread): > @Marc RJ Carlson

Leonardo Collado Torres (17:43:53) (in thread): > I got beyond the point where it started crashing for the presenters (@Eric Davisand@Wancen Mu) - File (PNG): Screen Shot 2022-07-27 at 2.43.07 PM.png

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Leonardo Collado Torres (17:44:16) (in thread): > so yeah, likely nothing@Sean Daviscan do from the Orchestra side

Leonardo Collado Torres (17:48:54) (in thread): > Ok, I got as far as this parthttps://community-bioc.slack.com/archives/CC88GP2F4/p1658958497015369. So yeah, something from the local firewall is getting in the way - Attachment: Attachment > ```> ## split sparse count matrix into NumericList > > rna <- rna_Granges[-which(rna.sd==0)] %>% > + mutate(counts1 = NumericList(asplit(rna.scaled, 1)))%>% sort() > Error in h(simpleError(msg, call)) : > error in evaluating the argument ‘x’ in selecting a method for function ‘sort’: object ‘rna_Granges’ not found > > traceback() > 5: h(simpleError(msg, call)) > 4: .handleSimpleError(function (cond) > .Internal(C_tryCatchHelper(addr, 1L, cond)), “object ‘rna_Granges’ not found”, > base::quote(mutate(., counts1 = NumericList(asplit(rna.scaled, > 1))))) > 3: mutate(., counts1 = NumericList(asplit(rna.scaled, 1))) > 2: sort(.) > 1: rna_Granges[-which(rna.sd == 0)] %>% mutate(counts1 = NumericList(asplit(rna.scaled, > 1))) %>% sort() > > options(width = 120) > > sessioninfo::session_info() > ─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────── > setting value > version R version 4.2.0 (2022-04-22) > os Ubuntu 20.04.4 LTS > system x86_64, linux-gnu > ui RStudio > language (EN) > collate en_US.UTF-8 > ctype en_US.UTF-8 > tz Etc/UTC > date 2022-07-27 > rstudio 2022.02.3+492 Prairie Trillium (server) > pandoc 2.17.1.1 @ /usr/local/bin/pandoc > > ─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────── > package * version date (UTC) lib source > AnnotationDbi 1.59.1 2022-05-19 [1] Bioconductor > AnnotationHub * 3.5.0 2022-04-26 [1] Bioconductor > assertthat 0.2.1 2019-03-21 [1] RSPM (R 4.2.0) > Biobase * 2.57.1 2022-05-19 [1] Bioconductor > BiocFileCache * 2.5.0 2022-04-26 [1] Bioconductor > BiocGenerics * 0.43.0 2022-04-26 [1] Bioconductor > BiocIO 1.7.1 2022-05-06 [1] Bioconductor > BiocManager 1.30.18 2022-05-18 [1] CRAN (R 4.2.0) > BiocParallel 1.31.10 2022-07-07 [1] Bioconductor > BiocVersion 3.16.0 2022-04-26 [1] Bioconductor > Biostrings 2.65.1 2022-06-09 [1] Bioconductor > bit 4.0.4 2020-08-04 [1] RSPM (R 4.2.0) > bit64 4.0.5 2020-08-30 [1] RSPM (R 4.2.0) > bitops 1.0-7 2021-04-24 [1] RSPM (R 4.2.0) > blob 1.2.3 2022-04-10 [1] RSPM (R 4.2.0) > cachem 1.0.6 2021-08-19 [1] RSPM (R 4.2.0) > cli 3.3.0 2022-04-25 [1] RSPM (R 4.2.0) > codetools 0.2-18 2020-11-04 [2] CRAN (R 4.2.0) > colorspace 2.0-3 2022-02-21 [1] RSPM (R 4.2.0) > crayon 1.5.1 2022-03-26 [1] RSPM (R 4.2.0) > curl 4.3.2 2021-06-23 [1] RSPM (R 4.2.0) > data.table 1.14.2 2021-09-27 [1] RSPM (R 4.2.0) > DBI 1.1.3 2022-06-18 [1] RSPM (R 4.2.0) > dbplyr * 2.2.1 2022-06-27 [1] RSPM (R 4.2.0) > DelayedArray 0.23.0 2022-04-26 [1] Bioconductor > digest 0.6.29 2021-12-01 [1] RSPM (R 4.2.0) > dplyr 1.0.9 2022-04-28 [1] RSPM (R 4.2.0) > ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.2.0) > ExperimentHub * 2.5.0 2022-04-26 [1] Bioconductor > fansi 1.0.3 2022-03-24 [1] RSPM (R 4.2.0) > farver 2.1.1 2022-07-06 [1] CRAN (R 4.2.0) > fastmap 1.1.0 2021-01-25 [1] RSPM (R 4.2.0) > filelock 1.0.2 2018-10-05 [1] RSPM (R 4.2.0) > generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0) > GenomeInfoDb * 1.33.3 2022-05-10 [1] Bioconductor > GenomeInfoDbData 1.2.8 2022-05-03 [1] Bioconductor > GenomicAlignments 1.33.1 2022-07-22 [1] Bioconductor > GenomicRanges * 1.49.0 2022-04-26 [1] Bioconductor > ggplot2 * 3.3.6 2022-05-03 [1] RSPM (R 4.2.0) > ggridges * 0.5.3 2021-01-08 [1] RSPM (R 4.2.0) > glue 1.6.2 2022-02-24 [1] RSPM (R 4.2.0) > gtable 0.3.0 2019-03-25 [1] RSPM (R 4.2.0) > htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.0) > httpuv 1.6.5 2022-01-05 [1] RSPM (R 4.2.0) > httr 1.4.3 2022-05-04 [1] RSPM (R 4.2.0) > InteractionSet * 1.25.0 2022-04-26 [1] Bioconductor > interactiveDisplayBase 1.35.0 2022-04-26 [1] Bioconductor > IRanges * 2.31.0 2022-04-26 [1] Bioconductor > KEGGREST 1.37.3 2022-07-08 [1] Bioconductor > KernSmooth 2.23-20 2021-05-03 [2] CRAN (R 4.2.0) > knitr 1.39 2022-04-26 [1] RSPM (R 4.2.0) > ks 1.13.5 2022-04-14 [1] RSPM (R 4.2.0) > labeling 0.4.2 2020-10-20 [1] RSPM (R 4.2.0) > later 1.3.0 2021-08-18 [1] RSPM (R 4.2.0) > lattice 0.20-45 2021-09-22 [2] CRAN (R 4.2.0) > lifecycle 1.0.1 2021-09-24 [1] RSPM (R 4.2.0) > magrittr 2.0.3 2022-03-30 [1] RSPM (R 4.2.0) > MASS 7.3-58 2022-07-14 [1] CRAN (R 4.2.0) > Matrix 1.4-1 2022-03-23 [2] CRAN (R 4.2.0) > MatrixGenerics * 1.9.1 2022-06-24 [1] Bioconductor > matrixStats * 0.62.0 2022-04-19 [1] RSPM (R 4.2.0) > mclust 5.4.10 2022-05-20 [1] RSPM (R 4.2.0) > memoise 2.0.1 2021-11-26 [1] RSPM (R 4.2.0) > mime 0.12 2021-09-28 [1] RSPM (R 4.2.0) > munsell 0.5.0 2018-06-12 [1] RSPM (R 4.2.0) > mvtnorm 1.1-3 2021-10-08 [1] RSPM (R 4.2.0) > nullranges * 1.3.0 2022-04-26 [1] Bioconductor > nullrangesData * 1.3.0 2022-04-27 [1] Bioconductor > patchwork * 1.1.1 2020-12-17 [1] RSPM (R 4.2.0) > pillar 1.8.0 2022-07-18 [1] CRAN (R 4.2.0) > pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.2.0) > plyr 1.8.7 2022-03-24 [1] RSPM (R 4.2.0) > plyranges * 1.17.0 2022-04-26 [1] Bioconductor > png 0.1-7 2013-12-03 [1] RSPM (R 4.2.0) > pracma 2.3.8 2022-03-04 [1] RSPM (R 4.2.0) > promises 1.2.0.1 2021-02-11 [1] RSPM (R 4.2.0) > purrr * 0.3.4 2020-04-17 [1] RSPM (R 4.2.0) > R6 2.5.1 2021-08-19 [1] RSPM (R 4.2.0) > rappdirs 0.3.3 2021-01-31 [1] RSPM (R 4.2.0) > Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.2.0) > RCurl 1.98-1.7 2022-06-09 [1] RSPM (R 4.2.0) > restfulr 0.0.15 2022-06-16 [1] RSPM (R 4.2.0) > rjson 0.2.21 2022-01-09 [1] RSPM (R 4.2.0) > rlang 1.0.4 2022-07-12 [1] CRAN (R 4.2.0) > Rsamtools 2.13.3 2022-05-25 [1] Bioconductor > RSQLite 2.2.15 2022-07-17 [1] CRAN (R 4.2.0) > rstudioapi 0.13 2020-11-12 [1] RSPM (R 4.2.0) > rtracklayer 1.57.0 2022-04-26 [1] Bioconductor > S4Vectors * 0.35.1 2022-06-08 [1] Bioconductor > scales 1.2.0 2022-04-13 [1] RSPM (R 4.2.0) > sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.2.0) > shiny 1.7.2 2022-07-19 [1] CRAN (R 4.2.0) > speedglm 0.3-4 2022-02-24 [1] RSPM (R 4.2.0) > SummarizedExperiment * 1.27.1 2022-04-29 [1] Bioconductor > tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.0) > tidyr * 1.2.0 2022-02-01 [1] RSPM (R 4.2.0) > tidyselect 1.1.2 2022-02-21 [1] RSPM (R 4.2.0) > utf8 1.2.2 2021-07-24 [1] RSPM (R 4.2.0) > vctrs 0.4.1 2022-04-13 [1] RSPM (R 4.2.0) > withr 2.5.0 2022-03-03 [1] RSP…

Sean Davis (17:52:43) (in thread): > I think I fixed part of the problem, so those that were gettingBad Gatewayerrors are likely getting in again. The403errors are still likely firewall issues.

Leonardo Collado Torres (17:53:51) (in thread): > ohh ok, thanks Sean!!!

Alex Mahmoud (18:08:36): > @Alex Mahmoud has joined the channel

Wancen Mu (19:27:02) (in thread): > Thanks all for addressing this previously!

Leonardo Collado Torres (20:35:04): - File (JPEG): Image from iOS

Peter Hickey (21:20:19): > @Peter Hickey has joined the channel

Matthew McCall (22:47:22): > @Matthew McCall has joined the channel

2022-07-28

Kozo Nishida (03:15:38): > @Kozo Nishida has joined the channel

Helena L. Crowell (04:41:06): > @Helena L. Crowell has joined the channel

Mahmoud Ahmed (10:44:32): > @Mahmoud Ahmed has joined the channel

Alex Mahmoud (13:00:24): > Fwiw, the links in announcements on Socio website aren’t clickable or highlightable to copy (unless you go to the Developer Tools to copy the text from within the element), so in case it helps anyone to not have to manually type them: > Stickers:https://forms.gle/7ZVciDiY4XW6QDPNADay 1 survey:https://forms.gle/KrTu4hBJkmrpfEAK8Lightning talks:https://forms.gle/PKecuB8kfvcvM2ke9 - Attachment (Google Docs): BioC2022 Stickers > Thank you for attending the Bioconductor Conference 2022. If you would like a BioC2022 sticker mailed to you, please provide a mailing address. - Attachment (Google Docs): Bioc2022 - Post-conference survey > Thank you for attending the Bioconductor Conference 2022. The conference website is at https://bioc2022.bioconductor.org. Files and videos will be available on the BioC YouTube channel soon. If you would like a Bioc2022 sticker mailed to you please fill in your mailing details in the form https://forms.gle/UajfHrcyxbgBc9si7 - Attachment (Google Docs): BioC 2022 Lightning Talks > Lightning Talks will be held on Friday, July 29 at 10:00am Pacific time. Submit this form if you wish to present a 4 min Lightning Talk. The deadline for submission is Thursday July 28 at 1:00pm Pacific time. Slots will be assigned to participants on a first-come-first-served basis. Lightning Talks must strictly adhere to time. We recommend 5 or fewer slides.

Krithika Bhuvanesh (13:04:06): > Not able to share my slide (posters) on Jitsi. Anyone else having this issue ?

Krithika Bhuvanesh (13:11:32): > Hi everyone ! If you would like to learn how our Health Informatics and Data Science (HIDS) Masters Program at Georgetown uses R and Bioconductor in our courses, please join me at this link:https://meet.jit.si/BioCPosterSession7 - Attachment (meet.jit.si): Jitsi Meet > Join a WebRTC video conference powered by the Jitsi Videobridge

Sehyun Oh (13:14:32) (in thread): > Yes, same here.

Krithika Bhuvanesh (13:15:47) (in thread): > I first logged into my google chrome tab, and installed that Jitsi chrom extension. It then allowed me to share one of the chrome tabs . I still dont know the screen share works or not

Sehyun Oh (13:16:58) (in thread): > Yeah, I installed Jitsi chrome extension, but nothing changes. Do you know how to give a permission to camera/microphone for this app?

Krithika Bhuvanesh (13:17:27) (in thread): > i had to close and re-open my chrome window and then it asked me .

Hedia Tnani (15:13:45): > @Hedia Tnani has joined the channel

Hedia Tnani (15:31:45): > Hi

Hedia Tnani (15:32:03): > Are we having the kahoot in this channel?

Michael Love (15:43:05): > @Michael Love has joined the channel

Tim Triche (16:16:11): > what is a kahoot

Leonardo Collado Torres (16:20:36): > looks like a Trivia-like gamehttps://en.wikipedia.org/wiki/Kahoot! - Attachment: Kahoot! > Kahoot! is a game-based learning platform, used as educational technology in schools and other educational institutions. Its learning games, “kahoots”, are user-generated multiple-choice quizzes that can be accessed via a web browser or the Kahoot! app. Kahoot! can be used to review students’ knowledge, for formative assessment, or as a break from traditional classroom activities. Kahoot! also includes trivia quizzes. This educational platform is similar to other technological learning tools, such as Wooflash, Socrative, or Quizlet.

Leonardo Collado Torres (16:20:48): > @Hedia Tnanican likely tell you more about it

Mervin Fansler (17:17:55): > @Mervin Fansler has joined the channel

Sean Davis (18:20:00): > For those on site in Seattle, note that there was an error in the schedule - tidy transcriptomics is in Cure Auditorium at 3:30; Deploy custom Bioconductor data is in the Cure meeting room.

2022-07-29

Tanya Grancharova (10:33:25): > @Tanya Grancharova has joined the channel

Stephanie Hicks (11:55:24): > quick question – when I try to join the TAB link, it says the session has ended. Is there another way to join? I posted this on the “Wall” just now too - File (PNG): Screen Shot 2022-07-29 at 11.54.54 AM.png

Michael Love (11:57:15): > as a backup, we can just use my personal zoom, and I can record to cloud? Or wait for webex fix?

Stephanie Hicks (11:57:31): > @Michael Loveare you seeing the same?

Michael Love (11:57:47): > yeah and@Charlotte Sonesonand@Levi Waldron

Stephanie Hicks (11:57:54): > tagging@Erica Feickin case it’s helpful

Stephanie Hicks (12:00:59): > did we decide if there should be a back up zoom room?

Levi Waldron (12:03:11) (in thread): > Since some of the TAB is there in person I guess the A/V team needs to be in on the fix, but we could start our own meeting in the meantime anyways so they have the option of joining.

Levi Waldron (12:04:32): > Yeah let’s get together on Zoom and post the link until someone from Seattle tells us to do something else.

Jenny Drnevich (12:07:22): > Sorry, everyone. The link on Socio is wrong. We are trying to change it but this is the correct one:https://seattlechildrens.webex.com/seattlechildrens/j.php?MTID=mc4747ca76f3f5459bf732453835b5f3c - Attachment (Cisco Webex Site): Meet virtually with Cisco Webex. Anytime, anywhere, on any device. > Simple, modern video meetings for everyone on the world’s most popular and trusted collaboration platform.

Krithika Bhuvanesh (12:25:08): > Those who are compering/managing the session on stage , please introduce yourselves first ! Would be nice to connect a voice to a name / face ! Sometimes the camera is too zoomed out, other times we cannot make out the person if they are masked:slightly_smiling_face:

Tim Triche (12:30:47) (in thread): > This was a Socio glitch — sorry

Tim Triche (12:31:01) (in thread): > Fixed as of 9:05am:flushed:

Krithika Bhuvanesh (12:44:03): > There was an announcement just now that said “Nanostring poster is in 30min” - that is not correct. According to agenda, poster session is at 2:15pm Pacific

Erica Feick (12:46:16) (in thread): > That is correct, it is at 2:15pm. I will send out a correction.

Levi Waldron (12:53:14): > Lightning talks link is not working@Erica Feick@Marc RJ Carlson(update never mind!)

Stephanie Hicks (12:54:33) (in thread): > thank you@Tim Triche!:gratitude-thank-you:

Nitesh Turaga (15:20:52): > GPU talk public linkhttps://docs.google.com/presentation/d/1ss9kdDEkYUI405JH0Lc8eaD9y5jw9ADznLug8_h0zTA/edit?usp=drivesdk

Snehal Wani (16:10:46): > @Snehal Wani has joined the channel

Leonardo Collado Torres (16:30:01): > https://nanostring.com/wp-content/uploads/2022/07/SpatialOmicsOverlay.html

Leonardo Collado Torres (16:30:13): > I didn’t get the other link

Euphy Wu (16:31:26): > @Euphy Wu has joined the channel

Nicole Ortogero (16:32:07): > https://nanostring.com/products/geomx-digital-spatial-profiler/geoscript-hub/zzz#script-spatialomicsoverlay-package - Attachment (NanoString): GeoScript Hub > Available on GeoScript Hub Evaluate Normalization for Protein This script was designed for data from the GeoMx protein assay. It will also work with data

Leonardo Collado Torres (16:32:13): > thanks!

Nicole Ortogero (17:34:24): > Thanks again to those who joined the walking tour Wednesday. It was a blast! - File (JPEG): 20220727_192414.jpg

Kristyna Kupkova (20:07:02): > @Kristyna Kupkova has joined the channel

Claire Rioualen (20:20:53): > Thank you for organizing a great event! I’ll be a few more days in Seattle doing some “scientific tourism”, in case someone feels like joining:v:

Leonardo Collado Torres (20:54:45): > https://www.toasttab.com/nanasgreentea/v3/

Garth Kong (21:35:24): > Did anyone take the extra laptop charger? If it’s for a Dell computer then that’s likely mine:disappointed:

Chenchen Zhu (21:51:55): > @Chenchen Zhu has joined the channel

Marcel Ramos Pérez (22:10:07): > Some of us are going to Wild Ginger McKenzie(206) 707-0396https://maps.app.goo.gl/CrB8w71VpwHn1Pji6 - Attachment (google.com): Wild Ginger McKenzie · 2202B 8th Ave, Seattle, WA 98121 > ★★★★☆ · Southeast Asian restaurant

2022-07-30

Noor Pratap Singh (03:05:23): > @Noor Pratap Singh has joined the channel

Lori Shepherd (06:52:44) (in thread): > I think jenny might have grabbed it. I’ll tell her to get in touch with you

Jenny Drnevich (07:35:17) (in thread): > I do have it. And I found my charger in the one of the ~5000 compartments of my backpack that I apparently missed in all of my 3 frantic searches. I’ll DM you for your address and mail it

2022-07-31

mariadermit (02:44:43): > @mariadermit has joined the channel

2022-08-04

László Kupcsik (21:59:19): > @László Kupcsik has joined the channel

2022-08-08

kent riemondy (17:03:25): > @kent riemondy has left the channel

2022-08-15

Alexander Bender (07:17:54): > @Alexander Bender has joined the channel

2022-08-24

Erica Feick (07:25:06): > The videos from the BioC2022 conference are being loaded on to YouTube now- right now we have keynotes and short talks available. - Attachment (YouTube): BioC 2022 > Share your videos with friends, family, and the world

2022-09-12

Leonardo Collado Torres (14:30:24): > Hi@Erica Feick! Do you know if there are some talks that will be uploaded later on or are all talks that were going to be uploaded available now? (Like maybe not all were recorded or not everyone gave permission to upload them). For example, there’s one byTercen that I wanted to show to a colleague.

2022-09-13

Sean Davis (13:36:20) (in thread): > I just added a bunch (like 20) to the Bioc2022 Youtube channel, so you might check again. I don’t know the answer, though, as to if this is now the entire set.

2022-09-15

Leonardo Collado Torres (12:28:10) (in thread): > Thanks Sean! I just checked again and the talk I’m looking for isn’t there, but well, that’s ok. I’ll keep waiting or just ask my colleague to meet with the speaker directly

Erica Feick (14:30:40) (in thread): > Sorry for the delay@Leonardo Collado Torres, been out sick. I know some videos are still being processed but there were some issues of no audio with others - and I believe the Tercen talks was one of them. When I have an update on that I will let you know!

Leonardo Collado Torres (15:37:20) (in thread): > No worries and I hope that you are feeling better Erica! > > I see, ok, thanks for the info about the audio issues.

2022-09-19

Leonardo Collado Torres (10:22:18) (in thread): > @Erica FeickI just noticed that there are two playlists on the R Consortium website. One isBioc2022and the other one isBioC 2022https://www.youtube.com/playlist?list=PLdl4u5ZRDMQS4pReC0_sUnPMB3x9YIPkHhttps://www.youtube.com/playlist?list=PL4IzsxWztPdmXgSAjnKoEdDTgN7vOhBq0 - Attachment (YouTube): Bioc2022 > This playlist compiles the videos from the Bioconductor Conference 2022 held at Seattle Children’s Hospital in Seattle Washington. - Attachment (YouTube): BioC 2022 > Share your videos with friends, family, and the world

2022-09-20

Erica Feick (10:06:36) (in thread): > Ok I will have them take a look and see if they can consolidate.

2022-09-22

Sean Davis (08:27:20) (in thread): > @Leonardo Collado Torresand@Erica Feick, one playlist is the Bioconductor playlist and the other is the R Consortium playlist. That duplication is intentional so that we have the content on Bioconductor as in previous years.

Erica Feick (08:27:57) (in thread): > Thanks for clarifying Sean!

Leonardo Collado Torres (09:18:43) (in thread): > I see, but videos are not on both@Sean Davis. Some are only present in one playlist, like search “TREG” by@Louise Huuki

Sean Davis (10:03:41) (in thread): > The syncing is, unfortunately, done by hand and I’m a little behind since R consortium has been working on them on-and-off. I’ll work on finally syncing the list this weekend.

2022-10-06

Devika Agarwal (05:38:22): > @Devika Agarwal has joined the channel

2022-10-10

Mercilena Benjamin (13:55:12): > @Mercilena Benjamin has joined the channel

2022-10-18

Maria Doyle (08:45:49): > Does anyone know about this or if it can be fixed?https://twitter.com/enricoferrero/status/1582314622459465728 - Attachment (twitter): Attachment > @Bioconductor it looks like your #BioC2022 playlist on YouTube is incomplete and mixed up with R/Medicine, but luckily the R Consortium channel has the right one here: https://www.youtube.com/playlist?list=PL4IzsxWztPdmXgSAjnKoEdDTgN7vOhBq0

Mikhail Dozmorov (19:21:35) (in thread): > Should be fixed - both the websitehttps://bioc2022.bioconductor.org/schedule/and the BioC2022 playlisthttps://youtube.com/playlist?list=PLdl4u5ZRDMQS4pReC0_sUnPMB3x9YIPkHare now in sync with R Consortium. - Attachment (bioc2022.bioconductor.org): Schedule > Schedule - Attachment (YouTube): Bioc2022 > This playlist compiles the videos from the Bioconductor Conference 2022 held at Seattle Children’s Hospital in Seattle Washington.

2022-11-30

Matt Ritchie (21:14:35): > @Matt Ritchie has joined the channel

Matt Ritchie (21:20:49): > @Matt Ritchie has left the channel

2022-12-05

Lizhong Chen (17:50:10): > @Lizhong Chen has joined the channel

Lizhong Chen (17:52:17): > @Lizhong Chen has left the channel

2022-12-20

Levi Waldron (12:23:25): > <!channel>anyone interested in#bioc-conference-everyone, to be held as a hybrid conference in Boston on August 2-4 2023, should join#bioc-conference-everyone- I will archive this one.

Ludwig Geistlinger (18:18:24): > @Ludwig Geistlinger has joined the channel

Ludwig Geistlinger (18:23:15): > Hi I gave two short talks at Bioc2022: One on BugSigDB, and one on BioPlex. When browsing through the recordings on youtube, it seems that the video that is supposed to show the BugSigDB talk actually shows the BioPlex talk:https://www.youtube.com/watch?v=2CuTtoLmmFs&list=PLdl4u5ZRDMQS4pReC0_sUnPMB3x9YIPkH&index=15. Can this be fixed? - Attachment (YouTube): BugSigDB: Accelerating Human Microbiome Research

Stephanie Hicks (19:34:48): > @Stephanie Hicks has left the channel

Athena Chen (21:41:29): > @Athena Chen has left the channel

Peter Hickey (21:52:58): > @Peter Hickey has left the channel

2022-12-21

Alexander Bender (07:16:13): > @Alexander Bender has left the channel

Tim Triche (08:59:52): > @Tim Triche has left the channel

Kristyna Kupkova (11:50:01): > @Kristyna Kupkova has left the channel

Andres Wokaty (15:03:00): > @Andres Wokaty has left the channel

Erica Feick (18:09:06) (in thread): > These should be fixed now! Thanks for letting us know.

2022-12-22

Nils Eling (02:30:20): > @Nils Eling has left the channel

Ludwig Geistlinger (05:59:11) (in thread): > Great, thanks!

Noor Pratap Singh (09:08:09): > @Noor Pratap Singh has left the channel

2023-01-12

Ray Su (23:22:14): > @Ray Su has left the channel

2023-01-18

José Basílio (13:09:06): > @José Basílio has joined the channel

2023-02-06

Sehyun Oh (08:54:49): > @Sehyun Oh has left the channel

2023-03-10

Marcel Ramos Pérez (11:30:30): > archived the channel